Related papers: Technology dictates algorithms: Recent development…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
A substantial disadvantage of traditional learning is that all students follow the same learning sequence, but not all of them have the same background of knowledge, the same preferences, the same learning goals, and the same needs.…
Recently developed technologies to generate single-cell genomic data have made a revolutionary impact in the field of biology. Multi-omics assays offer even greater opportunities to understand cellular states and biological processes.…
With current hardware and software, a standard computer can now hold in RAM an index for approximate pattern matching on about half a dozen human genomes. Sequencing technologies have improved so quickly, however, that scientists will soon…
An overview of current multiple alignment systems to date are described.The useful algorithms, the procedures adopted and their limitations are presented.We also present the quality of the alignments obtained and in which cases(kind of…
The proliferation of Large Language Models (LLMs) in medicine has enabled impressive capabilities, yet a critical gap remains in their ability to perform systematic, transparent, and verifiable reasoning, a cornerstone of clinical practice.…
A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e., sequence-to-sequence mapping). Recent works replace the…
High-throughput sequencing (HTS) technologies have revolutionized the field of genomics, enabling rapid and cost-effective genome analysis for various applications. However, the increasing volume of genomic data generated by HTS…
Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…
Discovering new medicines is the hallmark of human endeavor to live a better and longer life. Yet the pace of discovery has slowed down as we need to venture into more wildly unexplored biomedical space to find one that matches today's high…
This paper presents a novel DNA sequences alignment method based on inverted index. Now most large scale information retrieval system are all use inverted index as the basic data structure. But its application in DNA sequence alignment is…
Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…
The human-associated microbiome is closely tied to human health and is of substantial clinical interest. Metagenomics-based tools are emerging for clinical diagnostics, tracking the spread of diseases, and surveillance of potential…
Identifying similar documents within extensive volumes of data poses a significant challenge. To tackle this issue, researchers have developed a variety of effective distributed computing techniques. With the advancement of computing power…
Recent tumor genome sequencing confirmed that one tumor often consists of multiple cell subpopulations (clones) which bear different, but related, genetic profiles such as mutation and copy number variation profiles. Thus far, one tumor has…
Much of the present-day Artificial Intelligence (AI) utilizes artificial neural networks, which are sophisticated computational models designed to recognize patterns and solve complex problems by learning from data. However, a major…
Alternative splicing is crucial in gene regulation, with significant implications in clinical settings and biotechnology. This review article compiles bioinformatics RNA-seq tools for investigating differential splicing; offering a detailed…
Metagenomics is an emerging field of molecular biology concerned with analyzing the genomes of environmental samples comprising many different diverse organisms. Given the nature of metagenomic data, one usually has to sequence the genomic…
The dose delivered to the planning target volume by proton beams is highly conformal, sparing organs at risk and normal tissues. New treatment planning systems adapted to spot scanning techniques have been recently proposed to…
The study identifies a clear evolution from traditional methods to more advanced machine learning approaches. Current algorithms face persistent challenges, including degraded image quality, damaged ridge structures, and background noise,…